Q-TOFMicro1.2.LED3.4.MassLynxMS/MSMS1.2.MS/MS3.SurveyScan1.512.54MCP591.592.593.MCP614.625.621.Nano2.LEDLEDLEDLEDLEDLEDLED3.4.WatersZ-Spray,Z,RFLens,,MassLynxMassLynxMasslynx,MSTune,MSTune,(ES+Source)(Quatrupole)(Timeofflight)Capillary1.MSTunePeakDisplay/Setupscope(100-1000)1sec0.1seccontinuum0.5sec2.CapillaryMCPFightTubePressforOperatePressforStandby.3.FightTube(500Readback5630)4.MCP(200ReadbackMCP)5.capillary6.GFP1pmol/ulinfusion7.MSTune,COLGAS(APIGAS),,(GFP)Syringepump(ul/min)5ul/min8.(GFPm/z=785.8423)1.MSTune,,:2..3.FunctionTOFMSTOFMSMS4.DataFormatCentroidContinuumMCA,CentroidContinuumMCAContinuum5.(StartMass)(EndMass)(Function)TOFMSMS(SetMass)6.RunDurationScanTimeInterScanDelay7.Start1.MassLynxChromatogramSpectrum2.Chromatogram3.4.5.6.7.Spectrum8.Processcombine9.Average1:1010.MS/MS1.MS/MSMSScan,2.,3.MSTune304.FunctionTOFMSMSSetMassStartMassEndStart5.MSMSMasslynx(SampleList)MSFileMSEdit(DDA)DDA,MSScan1.MSScanOK,,LC/MSLockSpray,ConeVoltage:Frequency:,ScanTime:MS(File/SaveAs)2.MS/MSMSMSOKSetMassm/zLowHighMassm/zES+ES-,LC/MSLockSpray,FrequencySetMassm/zConeVoltageCollisionEnergy10m/z30ScanTime-MS/MS(File/SaveAs)3.SurveyScan(DDA)MS/MSWatersMicromassQ-Tofmicro(datadependentacquisitionDDA)MSMS/MSMS/MSMSDDAMS(targetprecursorions)MS/MSMS/MSMSMassLynx(SampleList)MSFileMSFileMS(Methodeditor),(SampleList)DDA(SampleList)TunePageDDAMSMethodMSFileNewMSDDA.DDAwizardNext,,ProteomicsNext,,FinishCreateAcquisitionMSSurveyMS/MSPeakDetectionExcludeIncludeAdductsCollisionLockSprayAcquisitionMSSurvey(ES+)(ES-)DiscardMSsurveyscansthatdonotcontainionsselectedforMS/MSanalysisMSsurveyMS/MSMSm/zIntensityMSsurveyscanm/zThreshold(ioncounts/sec)(candidateprecursorions)ThresholdMSScanTime1secInter-SacnDelay0.1secDataFormat()ConeVoltageSTOPMS/MS:ThresholdMSReturntoMSSurveywhen:Intensityfallsbelowpeptide2-3counts/secm/z83-4ReturntoMSSurveyafter:MS/MSSwitchCriteria7Threshold23MS/MS1SwitchCriteria2SwitchCriteriaMS1MS/MS2SwitchCriteriaMS/MS7secThreshold021secsMSScanrateandInstrumentconditionforMS/MSScanTime1secInter-ScanDelay0.1secDataFormatConeVoltageIPRfileforMS/MSMS/MSPeakDetectionPeakSelectionChargeStatePeakDetectionMS/MSDeisotopePeakDetectionMS/MSDetectionWindowP+1(13C)P+2(13C2)MS/MS1Da+1+22DaChargeStatePeakSelect234UseadvancedoptionsforChargeStatePeakSelectNumberofComponents1-10060-80ToleranceWindowPeakExtractionWindowChargeStateCollisionEnergyDefaultCollisionenergyUseTunePageCollisionEnergyUseCollisionEnergyProfile5CollisionEnergyModifyAddDeleteNewSaveSaveAsUseChargeStateRecognitionCS1FileModifyAddDeleteNewSaveSaveAsExcludeDynamicPeakExclusionExcludepeakwidth1000mDaC13FixedPeakExclusion,MS/MSExcludefromrangeExcludefromfileNewAddDeleteSaveAsSaveIncludeIncludemassMS/MS2OnlyselectpeaksthatareontheincludelistincludelistMS/MSPreferentiallyselectpeaksthatareontheincludelistincludeListMS/MSIncludefromrangeMS/MS,IncludefromfileNewAddDeleteSaveAsSave(RetentionTimeCollisionEnergyConeVoltageChargeState),(nominalmassaccuracy)1.(Lteff)1.MSTuneCalibration/CalibrateInstrument,2.Default.calUncal.cal3.MSTune/Option/TDCSetting,TDCSetting,Lteff=10784.,2ng/mlLeucineEnkephalin5ul/min5.LeucineEnkephalin(m/z556.2771)200counts/sec6.Acquisition27.combine(30scans)centerM8.LteffLteff1078(M/556.2771)1/29.LteffTDCsettingLteff2.1.PEG,5ul/min2.PEG200counts/sec3.TunePageAcquisition24.combine(30scans)centerSavespectrum5.MSTuneCalibration/CalibrateInstrument6.PEGpeghnh47.Calibraion,Calibrate/FromFileTOFBrowsePEG8.BrowsePEGHistory9.OK10.residualerrors3mDa-11.TOF:File/SaveAsMCP1.I.MSTune:Options/VentII.MassLynxIII.EmbeddedPC,EPCQ-TOFmicroIV.2.I.II.Q-TOFmicroEmbeddedPC,EPCEPCHostPCIII.MassLynxMassLynxIV.V.:Options/Pump,VacuumVI.LEDVII.MCPMCPMCP3.MCPI.310-6mbarII.CapillaryFlightTubeMCP0III.OperateIV.FightTube(1000Readback3000)V.Options/MCPconditioningMCPVI.start100stop2700Duration600step5StartMCP4.I.Capillary0II.FlightTube3000III.MCPDetector500IV.5.I.standbyII.Capillary0III.FlightTube0IV.MCPDetector0V.